From 55b7c2c6bde6849fe85e60a36264f1be937ecf64 Mon Sep 17 00:00:00 2001
From: Jan Travnicek <Jan.Travnicek@fit.cvut.cz>
Date: Fri, 14 Apr 2017 20:26:51 +0200
Subject: [PATCH] full and linear index ranked bar notation
---
.../FullAndLinearIndexConstruction.cpp | 1 +
.../indexing/FullAndLinearIndexConstruction.h | 9 +++++
.../query/FullAndLinearIndexPatterns.cpp | 1 +
.../query/FullAndLinearIndexPatterns.h | 39 ++++++++++++++++++-
tests.aarbology.sh | 2 +
5 files changed, 51 insertions(+), 1 deletion(-)
diff --git a/alib2algo/src/arbology/indexing/FullAndLinearIndexConstruction.cpp b/alib2algo/src/arbology/indexing/FullAndLinearIndexConstruction.cpp
index 9203d13fb3..e29d4d88be 100644
--- a/alib2algo/src/arbology/indexing/FullAndLinearIndexConstruction.cpp
+++ b/alib2algo/src/arbology/indexing/FullAndLinearIndexConstruction.cpp
@@ -16,6 +16,7 @@ indexes::arbology::FullAndLinearIndex < std::ranked_symbol < DefaultSymbolType,
}
auto fullAndLinearIndexConstructionPrefixRankedTree = FullAndLinearIndexConstruction::RegistratorWrapper < indexes::arbology::FullAndLinearIndex < std::ranked_symbol < DefaultSymbolType, DefaultRankType > >, tree::PrefixRankedTree < > > ( FullAndLinearIndexConstruction::construct );
+auto fullAndLinearIndexConstructionPrefixRankedBarTree = FullAndLinearIndexConstruction::RegistratorWrapper < indexes::arbology::FullAndLinearIndex < std::ranked_symbol < DefaultSymbolType, DefaultRankType > >, tree::PrefixRankedBarTree < > > ( FullAndLinearIndexConstruction::construct );
} /* namespace indexing */
diff --git a/alib2algo/src/arbology/indexing/FullAndLinearIndexConstruction.h b/alib2algo/src/arbology/indexing/FullAndLinearIndexConstruction.h
index ff9bcddfea..ddf6bc72d1 100644
--- a/alib2algo/src/arbology/indexing/FullAndLinearIndexConstruction.h
+++ b/alib2algo/src/arbology/indexing/FullAndLinearIndexConstruction.h
@@ -11,6 +11,7 @@
#include <indexes/arbology/FullAndLinearIndex.h>
#include <tree/RankedTreeWrapper.h>
#include <tree/ranked/PrefixRankedTree.h>
+#include <tree/ranked/PrefixRankedBarTree.h>
#include <core/multipleDispatch.hpp>
#include <tree/properties/SubtreeJumpTable.h>
#include <stringology/indexing/PositionHeapNaive.h>
@@ -35,6 +36,9 @@ public:
template < class SymbolType, class RankType >
static indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankType > > construct ( const tree::PrefixRankedTree < SymbolType, RankType > & tree );
+
+ template < class SymbolType, class RankType >
+ static indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankType > > construct ( const tree::PrefixRankedBarTree < SymbolType, RankType > & tree );
};
template < class SymbolType, class RankType >
@@ -42,6 +46,11 @@ indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankTyp
return indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankType > > ( stringology::indexing::PositionHeapNaive::construct ( string::LinearString < std::ranked_symbol < SymbolType, RankType > > ( w ) ), tree::properties::SubtreeJumpTable::compute ( w ) );
}
+template < class SymbolType, class RankType >
+indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankType > > FullAndLinearIndexConstruction::construct ( const tree::PrefixRankedBarTree < SymbolType, RankType > & w ) {
+ return indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankType > > ( stringology::indexing::PositionHeapNaive::construct ( string::LinearString < std::ranked_symbol < SymbolType, RankType > > ( w ) ), tree::properties::SubtreeJumpTable::compute ( w ) );
+}
+
} /* namespace indexing */
} /* namespace arbology */
diff --git a/alib2algo/src/arbology/query/FullAndLinearIndexPatterns.cpp b/alib2algo/src/arbology/query/FullAndLinearIndexPatterns.cpp
index 7364576279..dde3553975 100644
--- a/alib2algo/src/arbology/query/FullAndLinearIndexPatterns.cpp
+++ b/alib2algo/src/arbology/query/FullAndLinearIndexPatterns.cpp
@@ -18,6 +18,7 @@ std::set < unsigned > FullAndLinearIndexPatterns::query ( const indexes::arbolog
}
auto fullAndLinearIndexPatternsPrefixRankedPattern = FullAndLinearIndexPatterns::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedPattern < > > ( FullAndLinearIndexPatterns::query );
+auto fullAndLinearIndexPatternsPrefixRankedBarPattern = FullAndLinearIndexPatterns::RegistratorWrapper < std::set < unsigned >, tree::PrefixRankedBarPattern < > > ( FullAndLinearIndexPatterns::query );
} /* namespace query */
diff --git a/alib2algo/src/arbology/query/FullAndLinearIndexPatterns.h b/alib2algo/src/arbology/query/FullAndLinearIndexPatterns.h
index 58a507d2b5..fb6e605437 100644
--- a/alib2algo/src/arbology/query/FullAndLinearIndexPatterns.h
+++ b/alib2algo/src/arbology/query/FullAndLinearIndexPatterns.h
@@ -10,7 +10,8 @@
#include <indexes/arbology/FullAndLinearIndex.h>
#include <tree/RankedTreeWrapper.h>
-#include <tree/ranked/PrefixRankedTree.h>
+#include <tree/ranked/PrefixRankedPattern.h>
+#include <tree/ranked/PrefixRankedBarPattern.h>
#include <core/multipleDispatch.hpp>
#include <global/GlobalData.h>
@@ -64,6 +65,9 @@ public:
template < class SymbolType, class RankType >
static std::set < unsigned > query ( const indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankType > > & compressedBitParallelTreeIndex, const tree::PrefixRankedPattern < SymbolType, RankType > & pattern );
+
+ template < class SymbolType, class RankType >
+ static std::set < unsigned > query ( const indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankType > > & compressedBitParallelTreeIndex, const tree::PrefixRankedBarPattern < SymbolType, RankType > & pattern );
};
template < class SymbolType, class RankType >
@@ -98,6 +102,39 @@ std::set < unsigned > FullAndLinearIndexPatterns::query ( const indexes::arbolog
return res;
}
+template < class SymbolType, class RankType >
+std::set < unsigned > FullAndLinearIndexPatterns::query ( const indexes::arbology::FullAndLinearIndex < std::ranked_symbol < SymbolType, RankType > > & fullAndLinearIndex, const tree::PrefixRankedBarPattern < SymbolType, RankType > & pattern ) {
+ std::vector < unsigned > rev ( fullAndLinearIndex.getString ( ).size ( ), ( unsigned ) -1 );
+
+ std::vector < std::vector < std::ranked_symbol < SymbolType, RankType > > > treePatternParts;
+ treePatternParts.push_back ( std::vector < std::ranked_symbol < SymbolType, RankType > > ( ) );
+ for ( typename std::vector < std::ranked_symbol < SymbolType, RankType > >::const_iterator symbolIter = pattern.getContent ( ).begin ( ); symbolIter != pattern.getContent ( ).end ( ); ++symbolIter ) {
+ if ( pattern.getSubtreeWildcard ( ) == * symbolIter ) {
+ treePatternParts.push_back ( std::vector < std::ranked_symbol < SymbolType, RankType > > ( ) );
+ ++ symbolIter;
+ } else {
+ treePatternParts.back ( ).push_back ( * symbolIter );
+ }
+ }
+
+ std::vector < std::pair < unsigned, unsigned > > prevOcc = FindOccurrences ( fullAndLinearIndex.getStringIndex ( ) , treePatternParts [ 0 ] );
+
+ for ( unsigned i = 1; i < treePatternParts.size ( ); ++ i ) {
+ for ( std::pair < unsigned, unsigned > & occurrence : prevOcc )
+ occurrence.second = fullAndLinearIndex.getJumps ( ) [ occurrence.second ];
+
+ if ( ! treePatternParts [ i ].empty ( ) )
+ prevOcc = MergeOccurrences ( prevOcc, FindOccurrences ( fullAndLinearIndex.getStringIndex ( ), treePatternParts [ i ] ), rev );
+ }
+
+ std::set < unsigned > res;
+ for ( const std::pair < unsigned, unsigned > & occurrence : prevOcc ) {
+ res.insert ( occurrence.first );
+ }
+
+ return res;
+}
+
} /* namespace query */
} /* namespace arbology */
diff --git a/tests.aarbology.sh b/tests.aarbology.sh
index 7bb7ce56e4..f3918ca479 100755
--- a/tests.aarbology.sh
+++ b/tests.aarbology.sh
@@ -410,6 +410,8 @@ function runTestNonlinearPatternEnds {
clearResults
}
+runTestPattern "Exact Pattern Matching Using Full And Linear Index (PrefixRankedBar)" "./aarbology2 -a fullAndLinearIndex -s <(./acast2 -t PrefixRankedBarTree -i \"\$SUBJECT_FILE\" ) | ./aquery2 -q fullAndLinearIndexPatterns -i - -p <( ./acast2 -t PrefixRankedBarPattern -i \"\$PATTERN_FILE\" ) | ./astat2 -p size"
+
runTestPattern "Exact Pattern Matching Using Full And Linear Index (PrefixRanked)" "./aarbology2 -a fullAndLinearIndex -s <(./acast2 -t PrefixRankedTree -i \"\$SUBJECT_FILE\" ) | ./aquery2 -q fullAndLinearIndexPatterns -i - -p <( ./acast2 -t PrefixRankedPattern -i \"\$PATTERN_FILE\" ) | ./astat2 -p size"
runTestPattern "Exact Pattern Matching Using Compressed Bit Vectors (PrefixRankedBar)" "./aarbology2 -a compressedBitParallelIndex -s <(./acast2 -t PrefixRankedBarTree -i \"\$SUBJECT_FILE\" ) | ./aquery2 -q compressedBitParallelismPatterns -i - -p <( ./acast2 -t PrefixRankedBarPattern -i \"\$PATTERN_FILE\" ) | ./astat2 -p size"
--
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